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Calcium in PDB 7mg7: Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac

Protein crystallography data

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac, PDB code: 7mg7 was solved by B.E.Partridge, P.H.Winegar, C.A.Mirkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.62 / 1.75
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 65.869, 70.4, 125.09, 90, 90, 90
R / Rfree (%) 18.6 / 21.5

Other elements in 7mg7:

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac (pdb code 7mg7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac, PDB code: 7mg7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7mg7

Go back to Calcium Binding Sites List in 7mg7
Calcium binding site 1 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:21.9
occ:1.00
O A:TYR12 2.3 21.3 1.0
OD2 A:ASP19 2.3 25.4 1.0
O A:HOH490 2.4 21.9 1.0
OD1 A:ASP10 2.4 21.2 1.0
OD1 A:ASN14 2.4 25.3 1.0
O A:HOH416 2.4 20.2 1.0
OD2 A:ASP10 2.4 19.2 1.0
CG A:ASP10 2.7 19.1 1.0
CG A:ASP19 3.4 25.2 1.0
CG A:ASN14 3.5 26.0 1.0
C A:TYR12 3.5 22.1 1.0
OD1 A:ASP19 3.8 23.9 1.0
N A:ASN14 4.0 24.4 1.0
CB A:ASN14 4.1 26.7 1.0
MN A:MN301 4.1 25.0 1.0
CB A:ASP10 4.2 18.9 1.0
CA A:TYR12 4.4 23.4 1.0
O A:HOH462 4.5 23.2 1.0
N A:PRO13 4.5 26.4 1.0
N A:TYR12 4.5 21.6 1.0
CA A:PRO13 4.5 28.6 1.0
CE1 A:HIS24 4.5 22.1 1.0
O A:ASP208 4.6 19.1 1.0
C A:PRO13 4.6 26.4 1.0
CB A:TYR12 4.6 21.6 1.0
ND2 A:ASN14 4.6 23.4 1.0
OD1 A:ASP208 4.6 21.3 1.0
CB A:ASP19 4.7 24.4 1.0
CB A:ARG228 4.7 23.5 1.0
CA A:ASN14 4.7 24.6 1.0
CA A:ARG228 4.7 21.7 1.0
O A:ARG228 4.8 21.7 1.0
NE2 A:HIS24 4.8 22.5 1.0
CD1 A:TYR12 4.9 23.4 1.0

Calcium binding site 2 out of 2 in 7mg7

Go back to Calcium Binding Sites List in 7mg7
Calcium binding site 2 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:23.4
occ:1.00
O B:TYR12 2.3 24.6 1.0
O B:HOH500 2.3 23.0 1.0
O B:HOH452 2.3 23.4 1.0
OD2 B:ASP19 2.4 26.9 1.0
OD1 B:ASP10 2.4 21.7 1.0
OD1 B:ASN14 2.4 24.4 1.0
OD2 B:ASP10 2.5 20.9 1.0
CG B:ASP10 2.7 17.4 1.0
CG B:ASP19 3.5 28.2 1.0
C B:TYR12 3.5 23.3 1.0
CG B:ASN14 3.5 28.3 1.0
OD1 B:ASP19 3.9 22.6 1.0
N B:ASN14 4.0 25.9 1.0
CB B:ASN14 4.1 29.6 1.0
MN B:MN301 4.2 27.3 1.0
CB B:ASP10 4.3 20.1 1.0
CA B:TYR12 4.3 25.8 1.0
N B:TYR12 4.4 22.9 1.0
N B:PRO13 4.5 27.5 1.0
O B:HOH425 4.5 25.8 1.0
CB B:TYR12 4.5 23.0 1.0
CA B:PRO13 4.5 27.8 1.0
O B:ASP208 4.6 23.6 1.0
C B:PRO13 4.6 26.3 1.0
CE1 B:HIS24 4.6 23.3 1.0
ND2 B:ASN14 4.6 25.4 1.0
OD1 B:ASP208 4.7 23.1 1.0
CB B:ASP19 4.7 27.0 1.0
CA B:ASN14 4.7 28.5 1.0
CB B:ARG228 4.7 26.1 1.0
CA B:ARG228 4.8 23.6 1.0
CD2 B:TYR12 4.9 25.2 1.0
O B:ARG228 4.9 25.5 1.0
NE2 B:HIS24 4.9 26.5 1.0
CD1 B:ILE17 5.0 49.5 1.0

Reference:

B.E.Partridge, P.H.Winegar, Z.Han, C.A.Mirkin. Redefining Protein Interfaces Within Protein Single Crystals with Dna Journal of the American 2021CHEMICAL Society.
DOI: 10.1021/JACS.1C04191
Page generated: Fri Jul 19 02:02:00 2024

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